Research workbench
Crystal structure of rig-I helicase-rd in complex with 24-mer blunt- end hairpin RNA
Analyse Crystal structure of rig-I helicase-rd in complex with 24-mer blunt- end… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F9F
- Type
- protein + RNA
- Length
- 4,172 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ATP-dependent RNA helicase DDX58; RNA (5'…
- EC
- 3.6.4.13
- UniProt
- O95786
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 7 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable ATP-dependent RNA helicase DDX58 (EC 3.6.4.13) | protein | 673 | 46% helix, 16% strand | O95786 |
| B, D, F, H, J, L | RNA (5'- R(*GP*AP*AP*UP*AP*UP*AP*AP*UP*AP*GP*UP*GP*AP*UP*AP*UP*UP*AP*UP*AP*UP* UP*C)-3') | rna | 24 | — | — |
| C | Probable ATP-dependent RNA helicase DDX58 (EC 3.6.4.13) | protein | 668 | 45% helix, 17% strand | O95786 |
| E | Probable ATP-dependent RNA helicase DDX58 (EC 3.6.4.13) | protein | 672 | 46% helix, 17% strand | O95786 |
| G | Probable ATP-dependent RNA helicase DDX58 (EC 3.6.4.13) | protein | 669 | 47% helix, 18% strand | O95786 |
| I | Probable ATP-dependent RNA helicase DDX58 (EC 3.6.4.13) | protein | 674 | 45% helix, 17% strand | O95786 |
| K | Probable ATP-dependent RNA helicase DDX58 (EC 3.6.4.13) | protein | 672 | 46% helix, 17% strand | O95786 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, C, E, G, I, K
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, G, H, I, J, K, L
- BU3 · (R,R)-2,3-butanediol · additive · 13 copies · chains A, B, C, D, E, G, H, I, K
- ETF · Trifluoroethanol · additive · 4 copies · chains A, E, G, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 954 | 0.87 | 0.88 | 85 | empty |
| 2 | 659 | 0.85 | 0.90 | 82 | MG, ETF |
| 3 | 606 | 0.85 | 0.90 | 81 | MG |
| 4 | 632 | 0.84 | 0.89 | 87 | BU3, MG |
| 5 | 551 | 0.83 | 0.89 | 71 | empty |
Interfaces
15 interfaces between chains.
- C–D · 1835 Ų buried · 30 hydrogen bonds · protein-nucleic
- G–H · 1807 Ų buried · 36 hydrogen bonds · protein-nucleic
- I–J · 1806 Ų buried · 37 hydrogen bonds · protein-nucleic
- K–L · 1795 Ų buried · 40 hydrogen bonds · protein-nucleic
- A–B · 1733 Ų buried · 35 hydrogen bonds · protein-nucleic
Compared structures
- 5F9F · Crystal structure of RIG-I helicase-RD in complex with 24-mer blunt-end hairpin RNA · the same entry in another collection · chain L against L, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O95786
- Elsewhere: RCSB PDB 5F9F · PDBe 5F9F · UniProt O95786
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